Lightnews — Scholar-powered news

Kyle Harrington @kyleharrington.com · 11h

This is awesome! Way to go William!!!

Stanford University @stanford.edu · 21h

Congratulations to 2025 #MacFellow William Tarpeh! The Stanford chemical engineer is working on sustainable and practical solutions to treat wastewater and recover valuable mineral resources.

🗞️: stanford.io/3IZIBqF

Reposted by Kyle Harrington

Morgan Schwartz @msschwartz21.bsky.social · 1d

#geff v1 is released! 🎉 GEFF is a zarr-based Graph Exchange File Format with special support for tracking applications in Python and Java. Thank you to all the amazing developers who contributed at the Janelia 2025 Trackathon! liveimagetrackingtools.org/geff/

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Kyle Harrington @kyleharrington.com · 6d

Howdy #arxiv folks, could someone please endorse my colleague Ambrose Carr on q-bio.QM for a preprint? Endorsement code O488JD

thank you!

Kyle Harrington @kyleharrington.com · 7d

—

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Kyle Harrington @kyleharrington.com · 19d

What about looking at the one person you're trying to make laugh via DM

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Reposted by Kyle Harrington

Jean-Yves Tinevez @jytinevez.bsky.social · 29d

Save the date! The @pasteur.fr Pasteur course on image analysis is announced:

It will happen from the 1st of June to the 5th 2026.

This year there will be only one track: the Early Career Investigator track (beginners). 👇

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Reposted by Kyle Harrington

Nature Methods @natmethods.nature.com · Aug 29

A standardized, realistic phantom dataset consisting of ground-truth annotations for 6 diverse complexes serves as a community resource for benchmarking cryo-ET algorithms.

www.nature.com/articles/s41...

A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods

A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...

www.nature.com

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Kyle Harrington @kyleharrington.com · Aug 26

Caroline Hemphill also wrote up a great blog post about the competition: www.czbiohub.org/life-science...

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Kyle Harrington @kyleharrington.com · Aug 26

Better ML for cryo-ET starts with better benchmarks.

We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.

The result: community models beat expert tools.

Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...

A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods

A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...

doi.org

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Kyle Harrington @kyleharrington.com · Aug 19

Is that an anvil?

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Reposted by Kyle Harrington

Juan Nunez-Iglesias @jni.codes · Aug 1

It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇

Australian Museum Eureka Prizes @eurekaprizes.bsky.social · Jul 30

@napari.org @jni.codes is a finalist in the @ardc.edu.au Eureka Prize for Excellence in Research Software.

Learn more: youtu.be/0g_MkTa_NwQ

#EurekaPrizes

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Reposted by Kyle Harrington

napari @napari.org · Jul 10

🚀The napari team is excited to announce our brand new development roadmap — a community-informed vision for the future of napari!

🔍Read the blog to learn about our process and priorities:
napari.org/island-dispa...

🗺️OR check out the roadmap itself on napari.org:
napari.org/stable/roadm...

napari roadmap blog post — napari blog documentation

napari.org

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Kyle Harrington @kyleharrington.com · Jul 2

If you post the frames in a thread then we can try scrolling really fast

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Reposted by Kyle Harrington

Fabrice Senger @senger.bsky.social · Jun 20

when you discover new tools and ideas via biorixv, sometimes you don't even notice when it is published, some great stuff here :
www.nature.com/articles/s41...

Polarity-JaM: an image analysis toolbox for cell polarity, junction and morphology quantification - Nature Communications

Studying cell polarity is often limited by the complexity and variety of image data. Polarity-JaM is a software suite streamlining cell polarity analysis with easy-to-use tools and interfaces demonstr...

www.nature.com

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Kyle Harrington @kyleharrington.com · Jun 10

bsky.app/profile/wais...

Ariel Waisman @waisman-ar.bsky.social · Jun 7

Try it yourself! The plugin, documentation, and example datasets are available at:
multichannel-nuclear-analysis.github.io

Special thanks to the StarDist team for their incredible segmentation algorithm that made this possible.
#ImageAnalysis #FIJI #ImageJ #Microscopy

Multichannel Nuclear Analysis plugin

An ImageJ/FIJI plugin for analyzing multi-channel fluorescence images with a focus on nuclear segmentation using StarDist. https://multichannel-nuclear-analysis.github.io/

multichannel-nuclear-analysis.github.io

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Kyle Harrington @kyleharrington.com · May 16

There is a @napari.org hackathon at GloBIAS!

Be there or be square (or whatever layer type you'd like)

napari @napari.org · May 16

Reminder: if you go to the GloBIAS conference we can help you contribute to napari at the hackathon! A bunch of the team will be there! (Great thanks to the GloBIAS team for accommodating us!!!)

More details on the conference website.

GloBIAS @globias.bsky.social · May 15

Deadlines extended - you can still register for the GloBIAS conference! We have extended most deadlines. Please check our webpage: tinyurl.com/mr3kx5a5! Looking forward to welcoming you to Kobe, for training, developing and discussing a broad range of BIA topics!

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Kyle Harrington @kyleharrington.com · May 6

TFW you discover the internet in the conference venue isn't stable enough for a Google Slides presentation with videos 😅 luckily with >24hr warning

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Reposted by Kyle Harrington

napari @napari.org · May 1

And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵

a woman in a hat is crying and says " i 've traveled a good many miles to get here "

Alt: Charlotte from the Sanditon TV series, emotionally exclaiming, "I've traveled a good many miles to get here!"

media.tenor.com

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Kyle Harrington @kyleharrington.com · Apr 26

We have a suite for studying cell polarity in Python polarityjam.readthedocs.io feel free to post an issue if you need any more functionality

Python Segmentation API — polarityjam documentation

polarityjam.readthedocs.io

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Reposted by Kyle Harrington

Ricardo D. Righetto @lifeonthewedge.bsky.social · Apr 23

We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!

Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵

#CryoET #TeamTomo
www.biorxiv.org/content/10.1...

Figure 4. MemBrain v2 end-to-end workflow detects periodic phycobilisome organization. A: Raw tomogram slice of EMD-31244. B: Out-of-the-box MemBrain-seg segmentation (light blue). C: A single membrane instance can be visualized in Surforama and manually annotated with GT phycobilisome positions (magenta). D: MemBrain-pick localizes particles (trained with data from C) on all membranes in the tomogram. E: MemBrain-stats computes Ripley’s O statistic using the positions from D with a bin size of 5nm. The distance between peaks (35 nm) was measured to estimate chain unit spacings.

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Reposted by Kyle Harrington

Ben Engel @cellarchlab.com · Apr 24

Yo #TeamTomo, check out our updated #MemBrain v2 preprint. And better yet, give it a whirl on your #CryoET membranes! Please send us your feedback! 🧪🧶🧬🔬

Ricardo D. Righetto @lifeonthewedge.bsky.social · Apr 23

We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!

Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵

#CryoET #TeamTomo
www.biorxiv.org/content/10.1...

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Kyle Harrington @kyleharrington.com · Apr 7

"no no, I said turn up the economy"

Caitlin G. DeAngelis @caitlindeangelis.bsky.social · Apr 7

you know things are going well when they break out the turnip photos

photo of a red shopping basket filled with turnips, under the headline:
If you’re worried about food tariffs, adopt a frugal mindset and cook smarter
Learn to shop for groceries like a thrifter and work on eliminating waste
By Sheryl Julian Globe Correspondent,Updated April 7, 2025, 7:21 a.m.

caption: The big question is, writes Sheryl Julian, are we expected to remove all the pleasures from the table and turn the nightly dinner into a feast of locally grown turnips (above) and leafy greens?Jessica Rinaldi/Globe Staff

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Kyle Harrington @kyleharrington.com · Mar 6

Check this out!!! The results from our CryoET particle picking competition are available, the full test data (public and private datasets) is available, and you can dive right into the data on the CZ CryoET Data Portal! Enjoy and please let us know what you think :)

Utz Ermel @uermel.bsky.social · Mar 6

Results from CZII's #cryoET object detection challenge on kaggle are in!

Participation exceeded our expectations with 931 Teams from 76 countries competing, generating over 27,000 submissions. For an overview check out our post-competition page: cryoetdataportal.czscience.com/competition

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Kyle Harrington @kyleharrington.com · Mar 5

Awesome! So glad to see my former RL professor Andy Barto get this recognition (and Rich is too!)

Kosta Derpanis @csprofkgd.bsky.social · Mar 5

ACM A.M. Turing Award Honors 2024: Andrew Barto and Richard Sutton Recognized as Pioneers of Reinforcement Learning

awards.acm.org/about/2024-t...

Andrew Barto and Richard Sutton are the recipients of the 2024 ACM A.M. Turing Award for developing the conceptual and algorithmic foundations of reinforcement learning.

Andrew Barto and Richard Sutton as the recipients of the 2024 ACM A.M. Turing Award for developing the conceptual and algorithmic foundations of reinforcement learning. In a series of papers beginning...

awards.acm.org

Kyle Harrington @kyleharrington.com · Feb 12

Last night we were doing a family dance party...

My smartwatch gave a notification...

You've been running for 5 minutes...

I feel judged.

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